Irregular oscillations and symmetry breaking in a ring of coupled cells with yeast extract

Manuscript and open dataset for the manuscript.Abstract:Our work is focused on finding discrete non-uniform stationary states applicable for chemical computing and oscillations in a ring of coupled cells with glycolytic oscillatory reaction and equal transport rates for all chemical species. The cells (cuvettes) are fed by the Select Yeast Extract Y1625 and D-glucose solution, both enhanced by NaHCO3. The ring of coupled cells is formed by the two cuvettes and two capillaries. The mutual mass exchange is realized via reciprocal peristaltic pumping. The dynamic states of both cuvettes are measured by UV-Vis spectrophotometers at absorbance level of NADH (340 nm). We report an observation of in-phase, anti-phase, and phase-shifted glycolytic oscillations and transitions between uniform oscillations and chimera-like states occurring from an in-phase oscillatory system.We also performed an analysis of stability and bifurcations of stationary states in a model of twenty coupled cells in a cyclic array using the core model of glycolysis. Cells 1 and 11 represent main flow reactors (CSTRs) in the model with a much higher volume than cells 2-10 and 12-20, which approximate the capillaries mediating mass exchange between cells 1 and 11 as a cascade of small CSTRs. A bifurcation diagram in a plane of an inhibition rate coefficient (sigma_inh) and a transport rate coefficient (kd) is used to show the parameter region of occurrence of discrete non-uniform stationary states. We describe and mathematically simulate the mechanism of switching between them, establishing a chemical computing technique (working as AND/NOR logic gate). The ring of twenty coupled cells offers the same logic functions as two coupled cells.

本论文手稿及其配套开放数据集。摘要：本研究旨在探索适用于化学计算的离散非均匀定态，以及由糖酵解振荡反应构成、且所有化学物种输运速率均等的耦合细胞环体系中的振荡现象。实验所用的细胞（比色皿，cuvettes）采用添加了碳酸氢钠（NaHCO₃）的选择性酵母提取物Y1625与D-葡萄糖混合溶液进行供养。该耦合细胞环由2个比色皿与2根毛细管构成，细胞间的物质交换通过双向蠕动泵实现。两个比色皿的动态状态通过紫外-可见分光光度计（UV-Vis spectrophotometers），基于烟酰胺腺嘌呤二核苷酸（还原型，NADH）在340 nm波长下的吸光度进行测定。我们观测到了同相、反相以及相移型糖酵解振荡，同时观测到同相振荡体系可演化为均匀振荡与类嵌合态（chimera-like states），并存在二者之间的转变过程。本研究同时基于糖酵解核心模型（core model of glycolysis），对由20个耦合细胞组成的环状阵列模型的定态稳定性与分岔特性进行了分析。模型中的1号与11号细胞为主体流动反应器（连续搅拌釜式反应器，CSTRs），其体积远大于2-10号及12-20号细胞；后者以小型连续搅拌釜式反应器的级联结构，模拟介导1号与11号细胞间物质交换的毛细管。本研究以抑制速率系数（sigma_inh）与输运速率系数（kd）构成的参数平面绘制分岔图，以此展示离散非均匀定态的出现参数区间。我们对这些定态间的切换机制进行了描述与数学模拟，由此构建了可作为与门（AND）、或非门（NOR）逻辑门运行的化学计算技术。由20个耦合细胞构成的环状体系，可实现与2个耦合细胞环体系相同的逻辑功能。